SOAPdenovo-1.05-3.spec

Summary:    SOAP de novo - Short Oligonucleotide Analysis Package
Name:       soap
Version:    1.05
Release:    3
License:    GPLv3
Vendor:     BGI
Group: Applications/Life Sciences
Source:     SOAPdenovo-V1.05.src.tgz
Packager:   TACC - vaughn@tacc.utexas.edu
# This is the actual installation directory - Careful
BuildRoot:  /var/tmp/%{name}-%{version}-buildroot


#------------------------------------------------
# BASIC DEFINITIONS
#------------------------------------------------
%include rpm-dir.inc
%include ../system-defines.inc

# Compiler Family Definitions
# %include compiler-defines.inc
# MPI Family Definitions
# %include mpi-defines.inc
# Other defs

%define PNAME %{name}
%define INSTALL_DIR %{APPS}/%{name}/%{version}
%define MODULE_DIR  %{APPS}/%{MODULES}/%{name}

%define MODULE_VAR TACC_SOAP

#------------------------------------------------
# PACKAGE DESCRIPTION
#------------------------------------------------
%description

##
## PREP
##
# Use -n <name> if source file different from <name>-<version>.tar.gz
%prep
rm -rf $RPM_BUILD_ROOT/%{INSTALL_DIR}

##
## SETUP
##

%setup -n SOAPdenovo-V1.05

##
## BUILD
##

%build

#------------------------------------------------
# INSTALL SECTION
#------------------------------------------------
%install

%include ../system-load.inc
mkdir -p $RPM_BUILD_ROOT/%{INSTALL_DIR}

# Load correct compiler
# %include compiler-load.inc
# Load correct mpi stack
# %include mpi-load.inc
# %include mpi-env-vars.inc
# Load additional modules here (as needed)

module purge
module load TACC
#module swap $TACC_FAMILY_COMPILER gcc/4.7.1

make

cp -rp ./bin/* $RPM_BUILD_ROOT/%{INSTALL_DIR}

# ADD ALL MODULE STUFF HERE
# TACC module

rm   -rf $RPM_BUILD_ROOT/%{MODULE_DIR}
mkdir -p $RPM_BUILD_ROOT/%{MODULE_DIR}
cat > $RPM_BUILD_ROOT/%{MODULE_DIR}/%{version}.lua << 'EOF'
help (
[[
This module loads %{name}. SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for the human-sized genomes. The program is specially designed to assemble Illumina GA short reads. It creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost effective way. 

Please note:
- The 31mer version only supports kmers 31 in length or less.
- The 63mer version only supports kmers 63 in length or less and doubles the 
  memory consumption than 31mer version, even being used with kmers less than 31.
- The 127mer version only supports kmers 127 in length and double the 
  memory consumption than 63mer version, even being used with kmers less than 63.

Version %{version}
]])

whatis("Name: soap")
whatis("Version: %{version}")
whatis("Category: computational biology, genomics")
whatis("Keywords: Biology, Genomics, Assembly")
whatis("Description: ssake - a genomics application for assembling millions of very short DNA sequences")
whatis("URL: http://soap.genomics.org.cn/soapdenovo.html")

setenv("%{MODULE_VAR}_DIR","%{INSTALL_DIR}/")
prepend_path("PATH"       ,"%{INSTALL_DIR}/")

EOF

#--------------
#  Version file.
#--------------

cat > $RPM_BUILD_ROOT%{MODULE_DIR}/.version.%{version} << 'EOF'
#%Module3.1.1#################################################
##
## version file for %{PNAME}-%{version}
##

set     ModulesVersion      "%{version}"
EOF



#------------------------------------------------
# FILES SECTION
#------------------------------------------------
%files

# Define files permisions, user and group
%defattr(755,root,root,-)
%{INSTALL_DIR}
%{MODULE_DIR}

#------------------------------------------------
# CLEAN UP SECTION
#------------------------------------------------
%post
%clean
# Make sure we are not within one of the directories we try to delete
cd /tmp

# Remove the installation files now that the RPM has been generated
rm -rf $RPM_BUILD_ROOT